ROL_MajExp__rnaseq_051525

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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        ROL_MajExp__rnaseq_051525

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        This report has been generated by the nf-core/rnaseq analysis pipeline. For information about how to interpret these results, please see the documentation.

        Report generated on 2025-05-16, 01:10 PDT based on data in: /nfs3/Sharpton_Lab/prod/prod_restructure/projects/sielerjm/ZF__MajorExp/Transcriptomics/Code/Nextflow/work/8d/22dba793d631bd2366b5f178f41a02


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        General Statistics

        Showing 0/216 rows and 9/18 columns.
        Sample Name% AlignedM AlignedLibrary typesCFRM BiasDupsGCAvg lenMedian lenFailedSeqsTrimmed basesDupsGCAvg lenMedian lenFailedSeqs
        TS047_RoL_RNA_110
        84.3%
        24.1M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_110_1
        70.3%
        45.0%
        101bp
        101bp
        18%
        28.6M
        1.3%
        70.4%
        45.0%
        100bp
        100bp
        18%
        28.6M
        TS047_RoL_RNA_110_2
        70.5%
        45.0%
        101bp
        101bp
        18%
        28.6M
        1.4%
        70.5%
        45.0%
        99bp
        100bp
        18%
        28.6M
        TS047_RoL_RNA_112
        88.1%
        22.3M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_112_1
        73.1%
        46.0%
        101bp
        101bp
        9%
        25.4M
        1.3%
        73.1%
        46.0%
        100bp
        100bp
        18%
        25.3M
        TS047_RoL_RNA_112_2
        72.9%
        46.0%
        101bp
        101bp
        18%
        25.4M
        1.4%
        73.0%
        46.0%
        99bp
        100bp
        27%
        25.3M
        TS047_RoL_RNA_114
        85.7%
        24.3M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_114_1
        70.6%
        46.0%
        101bp
        101bp
        18%
        28.4M
        1.1%
        70.6%
        46.0%
        100bp
        100bp
        18%
        28.3M
        TS047_RoL_RNA_114_2
        70.5%
        46.0%
        101bp
        101bp
        18%
        28.4M
        1.2%
        70.6%
        46.0%
        100bp
        100bp
        18%
        28.3M
        TS047_RoL_RNA_116
        86.5%
        25.2M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_116_1
        72.1%
        46.0%
        101bp
        101bp
        18%
        29.2M
        1.2%
        72.1%
        46.0%
        100bp
        100bp
        27%
        29.1M
        TS047_RoL_RNA_116_2
        72.0%
        46.0%
        101bp
        101bp
        18%
        29.2M
        1.3%
        72.1%
        46.0%
        100bp
        100bp
        18%
        29.1M
        TS047_RoL_RNA_119
        89.3%
        21.3M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_119_1
        74.7%
        46.0%
        101bp
        101bp
        9%
        23.8M
        1.2%
        74.7%
        46.0%
        100bp
        100bp
        18%
        23.8M
        TS047_RoL_RNA_119_2
        74.8%
        46.0%
        101bp
        101bp
        18%
        23.8M
        1.3%
        74.9%
        46.0%
        100bp
        100bp
        18%
        23.8M
        TS047_RoL_RNA_136
        86.0%
        20.1M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_136_1
        70.0%
        46.0%
        101bp
        101bp
        18%
        23.4M
        1.2%
        70.0%
        46.0%
        100bp
        100bp
        18%
        23.4M
        TS047_RoL_RNA_136_2
        70.9%
        46.0%
        101bp
        101bp
        18%
        23.4M
        1.3%
        70.9%
        46.0%
        99bp
        100bp
        18%
        23.4M
        TS047_RoL_RNA_142
        86.7%
        22.7M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_142_1
        70.1%
        46.0%
        101bp
        101bp
        18%
        26.2M
        1.2%
        70.1%
        46.0%
        100bp
        100bp
        18%
        26.2M
        TS047_RoL_RNA_142_2
        70.5%
        46.0%
        101bp
        101bp
        18%
        26.2M
        1.3%
        70.5%
        46.0%
        100bp
        100bp
        18%
        26.2M
        TS047_RoL_RNA_145
        86.7%
        25.1M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_145_1
        72.4%
        45.0%
        101bp
        101bp
        18%
        29.0M
        1.2%
        72.4%
        46.0%
        100bp
        100bp
        18%
        29.0M
        TS047_RoL_RNA_145_2
        72.5%
        46.0%
        101bp
        101bp
        18%
        29.0M
        1.3%
        72.6%
        46.0%
        100bp
        100bp
        18%
        29.0M
        TS047_RoL_RNA_146
        88.0%
        26.7M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_146_1
        72.4%
        47.0%
        101bp
        101bp
        9%
        30.4M
        1.2%
        72.4%
        47.0%
        100bp
        100bp
        18%
        30.4M
        TS047_RoL_RNA_146_2
        72.5%
        47.0%
        101bp
        101bp
        18%
        30.4M
        1.3%
        72.6%
        47.0%
        100bp
        100bp
        18%
        30.4M
        TS047_RoL_RNA_16
        86.2%
        20.4M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_16_1
        73.8%
        45.0%
        101bp
        101bp
        27%
        23.7M
        1.3%
        73.8%
        45.0%
        99bp
        100bp
        27%
        23.7M
        TS047_RoL_RNA_16_2
        73.8%
        45.0%
        101bp
        101bp
        27%
        23.7M
        1.4%
        73.8%
        45.0%
        99bp
        100bp
        27%
        23.7M
        TS047_RoL_RNA_170
        88.5%
        22.9M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_170_1
        74.5%
        46.0%
        101bp
        101bp
        18%
        25.8M
        1.0%
        74.5%
        46.0%
        100bp
        100bp
        18%
        25.8M
        TS047_RoL_RNA_170_2
        74.8%
        46.0%
        101bp
        101bp
        18%
        25.8M
        1.2%
        74.8%
        46.0%
        100bp
        100bp
        18%
        25.8M
        TS047_RoL_RNA_175
        87.0%
        22.1M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_175_1
        72.1%
        46.0%
        101bp
        101bp
        18%
        25.4M
        1.2%
        72.1%
        46.0%
        100bp
        100bp
        18%
        25.4M
        TS047_RoL_RNA_175_2
        72.3%
        46.0%
        101bp
        101bp
        18%
        25.4M
        1.3%
        72.3%
        46.0%
        100bp
        100bp
        18%
        25.4M
        TS047_RoL_RNA_177
        88.4%
        21.3M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_177_1
        69.5%
        46.0%
        101bp
        101bp
        18%
        24.1M
        1.1%
        69.5%
        46.0%
        100bp
        100bp
        27%
        24.1M
        TS047_RoL_RNA_177_2
        69.6%
        46.0%
        101bp
        101bp
        27%
        24.1M
        1.3%
        69.6%
        46.0%
        100bp
        100bp
        27%
        24.1M
        TS047_RoL_RNA_20
        87.6%
        24.9M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_200
        87.8%
        30.2M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_200_1
        75.8%
        46.0%
        101bp
        101bp
        27%
        34.4M
        1.2%
        75.8%
        46.0%
        100bp
        100bp
        27%
        34.3M
        TS047_RoL_RNA_200_2
        75.9%
        46.0%
        101bp
        101bp
        27%
        34.4M
        1.3%
        76.0%
        46.0%
        100bp
        100bp
        27%
        34.3M
        TS047_RoL_RNA_204
        85.5%
        20.0M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_204_1
        73.6%
        45.0%
        101bp
        101bp
        18%
        23.4M
        1.3%
        73.6%
        45.0%
        99bp
        100bp
        27%
        23.4M
        TS047_RoL_RNA_204_2
        73.9%
        45.0%
        101bp
        101bp
        18%
        23.4M
        1.4%
        73.9%
        45.0%
        99bp
        100bp
        18%
        23.4M
        TS047_RoL_RNA_20_1
        73.2%
        46.0%
        101bp
        101bp
        18%
        28.4M
        1.3%
        73.3%
        46.0%
        99bp
        100bp
        18%
        28.4M
        TS047_RoL_RNA_20_2
        73.3%
        46.0%
        101bp
        101bp
        18%
        28.4M
        1.4%
        73.4%
        46.0%
        99bp
        100bp
        18%
        28.4M
        TS047_RoL_RNA_229
        89.6%
        25.8M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_229_1
        75.7%
        47.0%
        101bp
        101bp
        9%
        28.9M
        1.4%
        75.8%
        47.0%
        99bp
        100bp
        27%
        28.8M
        TS047_RoL_RNA_229_2
        76.2%
        47.0%
        101bp
        101bp
        18%
        28.9M
        1.5%
        76.2%
        47.0%
        99bp
        100bp
        18%
        28.8M
        TS047_RoL_RNA_231
        81.5%
        16.5M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_231_1
        69.9%
        45.0%
        101bp
        101bp
        27%
        20.3M
        1.5%
        69.9%
        45.0%
        99bp
        100bp
        27%
        20.3M
        TS047_RoL_RNA_231_2
        70.0%
        45.0%
        101bp
        101bp
        18%
        20.3M
        1.6%
        70.1%
        45.0%
        99bp
        100bp
        27%
        20.3M
        TS047_RoL_RNA_258
        85.7%
        22.6M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_258_1
        72.8%
        45.0%
        101bp
        101bp
        18%
        26.4M
        1.3%
        72.8%
        45.0%
        100bp
        100bp
        18%
        26.4M
        TS047_RoL_RNA_258_2
        72.9%
        45.0%
        101bp
        101bp
        18%
        26.4M
        1.4%
        73.0%
        46.0%
        99bp
        100bp
        18%
        26.4M
        TS047_RoL_RNA_262
        87.9%
        25.3M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_262_1
        74.6%
        46.0%
        101bp
        101bp
        9%
        28.8M
        1.2%
        74.6%
        46.0%
        100bp
        100bp
        18%
        28.8M
        TS047_RoL_RNA_262_2
        74.8%
        46.0%
        101bp
        101bp
        18%
        28.8M
        1.3%
        74.9%
        46.0%
        99bp
        100bp
        18%
        28.8M
        TS047_RoL_RNA_286
        87.0%
        21.9M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_286_1
        68.5%
        46.0%
        101bp
        101bp
        9%
        25.2M
        1.1%
        68.6%
        46.0%
        100bp
        100bp
        27%
        25.2M
        TS047_RoL_RNA_286_2
        68.8%
        46.0%
        101bp
        101bp
        27%
        25.2M
        1.2%
        68.8%
        46.0%
        100bp
        100bp
        27%
        25.2M
        TS047_RoL_RNA_288
        87.9%
        22.6M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_288_1
        70.1%
        46.0%
        101bp
        101bp
        18%
        25.7M
        1.1%
        70.1%
        46.0%
        100bp
        100bp
        27%
        25.7M
        TS047_RoL_RNA_288_2
        70.4%
        46.0%
        101bp
        101bp
        27%
        25.7M
        1.2%
        70.4%
        46.0%
        100bp
        100bp
        27%
        25.7M
        TS047_RoL_RNA_289
        87.1%
        26.4M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_289_1
        72.1%
        46.0%
        101bp
        101bp
        9%
        30.4M
        1.1%
        72.1%
        46.0%
        100bp
        100bp
        18%
        30.3M
        TS047_RoL_RNA_289_2
        72.3%
        46.0%
        101bp
        101bp
        27%
        30.4M
        1.3%
        72.3%
        46.0%
        100bp
        100bp
        27%
        30.3M
        TS047_RoL_RNA_291
        86.6%
        21.7M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_291_1
        65.2%
        46.0%
        101bp
        101bp
        18%
        25.1M
        1.1%
        65.2%
        46.0%
        100bp
        100bp
        18%
        25.1M
        TS047_RoL_RNA_291_2
        65.3%
        46.0%
        101bp
        101bp
        18%
        25.1M
        1.2%
        65.4%
        46.0%
        100bp
        100bp
        18%
        25.1M
        TS047_RoL_RNA_317
        85.1%
        21.5M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_317_1
        73.6%
        45.0%
        101bp
        101bp
        18%
        25.3M
        1.2%
        73.6%
        45.0%
        100bp
        100bp
        18%
        25.3M
        TS047_RoL_RNA_317_2
        74.1%
        45.0%
        101bp
        101bp
        18%
        25.3M
        1.3%
        74.2%
        45.0%
        100bp
        100bp
        18%
        25.3M
        TS047_RoL_RNA_318
        87.3%
        23.4M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_318_1
        72.7%
        46.0%
        101bp
        101bp
        18%
        26.8M
        1.2%
        72.7%
        46.0%
        100bp
        100bp
        27%
        26.8M
        TS047_RoL_RNA_318_2
        73.2%
        46.0%
        101bp
        101bp
        18%
        26.8M
        1.3%
        73.3%
        46.0%
        100bp
        100bp
        18%
        26.8M
        TS047_RoL_RNA_319
        86.3%
        23.8M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_319_1
        71.7%
        46.0%
        101bp
        101bp
        18%
        27.6M
        1.1%
        71.7%
        46.0%
        100bp
        100bp
        27%
        27.5M
        TS047_RoL_RNA_319_2
        71.8%
        46.0%
        101bp
        101bp
        18%
        27.6M
        1.2%
        71.8%
        46.0%
        100bp
        100bp
        18%
        27.5M
        TS047_RoL_RNA_322
        86.8%
        25.1M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_322_1
        72.4%
        46.0%
        101bp
        101bp
        18%
        28.9M
        1.1%
        72.4%
        46.0%
        100bp
        100bp
        18%
        28.9M
        TS047_RoL_RNA_322_2
        72.5%
        46.0%
        101bp
        101bp
        18%
        28.9M
        1.2%
        72.6%
        46.0%
        100bp
        100bp
        18%
        28.9M
        TS047_RoL_RNA_326
        84.0%
        20.3M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_326_1
        69.8%
        45.0%
        101bp
        101bp
        18%
        24.2M
        1.3%
        69.8%
        46.0%
        100bp
        100bp
        27%
        24.1M
        TS047_RoL_RNA_326_2
        70.0%
        46.0%
        101bp
        101bp
        27%
        24.2M
        1.4%
        70.0%
        46.0%
        99bp
        100bp
        27%
        24.1M
        TS047_RoL_RNA_328
        86.0%
        25.7M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_328_1
        70.9%
        46.0%
        101bp
        101bp
        9%
        29.9M
        1.2%
        70.9%
        46.0%
        100bp
        100bp
        18%
        29.8M
        TS047_RoL_RNA_328_2
        71.0%
        46.0%
        101bp
        101bp
        18%
        29.9M
        1.3%
        71.0%
        46.0%
        100bp
        100bp
        18%
        29.8M
        TS047_RoL_RNA_347
        86.4%
        20.0M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_347_1
        69.9%
        46.0%
        101bp
        101bp
        9%
        23.1M
        1.3%
        69.9%
        46.0%
        99bp
        100bp
        18%
        23.1M
        TS047_RoL_RNA_347_2
        70.1%
        46.0%
        101bp
        101bp
        9%
        23.1M
        1.4%
        70.1%
        46.0%
        99bp
        100bp
        9%
        23.1M
        TS047_RoL_RNA_355
        79.7%
        15.8M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_355_1
        71.9%
        45.0%
        101bp
        101bp
        27%
        19.8M
        1.8%
        71.9%
        45.0%
        99bp
        100bp
        18%
        19.8M
        TS047_RoL_RNA_355_2
        72.3%
        45.0%
        101bp
        101bp
        18%
        19.8M
        1.9%
        72.3%
        45.0%
        99bp
        100bp
        18%
        19.8M
        TS047_RoL_RNA_377
        90.2%
        21.7M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_377_1
        76.3%
        47.0%
        101bp
        101bp
        9%
        24.1M
        1.2%
        76.4%
        47.0%
        100bp
        100bp
        27%
        24.1M
        TS047_RoL_RNA_377_2
        76.7%
        47.0%
        101bp
        101bp
        27%
        24.1M
        1.3%
        76.8%
        47.0%
        100bp
        100bp
        27%
        24.1M
        TS047_RoL_RNA_381
        85.4%
        21.6M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_381_1
        72.9%
        45.0%
        101bp
        101bp
        27%
        25.3M
        1.2%
        72.9%
        45.0%
        100bp
        100bp
        18%
        25.3M
        TS047_RoL_RNA_381_2
        72.7%
        45.0%
        101bp
        101bp
        27%
        25.3M
        1.3%
        72.8%
        45.0%
        100bp
        100bp
        27%
        25.3M
        TS047_RoL_RNA_407
        92.7%
        28.4M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_407_1
        83.5%
        46.0%
        101bp
        101bp
        9%
        30.6M
        1.1%
        83.6%
        47.0%
        100bp
        100bp
        18%
        30.6M
        TS047_RoL_RNA_407_2
        83.9%
        47.0%
        101bp
        101bp
        18%
        30.6M
        1.2%
        84.0%
        47.0%
        100bp
        100bp
        18%
        30.6M
        TS047_RoL_RNA_412
        88.2%
        23.1M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_412_1
        75.2%
        46.0%
        101bp
        101bp
        9%
        26.2M
        1.1%
        75.2%
        46.0%
        100bp
        100bp
        18%
        26.2M
        TS047_RoL_RNA_412_2
        75.3%
        46.0%
        101bp
        101bp
        27%
        26.2M
        1.2%
        75.3%
        46.0%
        100bp
        100bp
        27%
        26.2M
        TS047_RoL_RNA_439
        84.6%
        20.5M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_439_1
        73.0%
        45.0%
        101bp
        101bp
        27%
        24.3M
        1.3%
        73.0%
        45.0%
        100bp
        100bp
        27%
        24.2M
        TS047_RoL_RNA_439_2
        73.1%
        45.0%
        101bp
        101bp
        36%
        24.3M
        1.4%
        73.2%
        45.0%
        99bp
        100bp
        36%
        24.2M
        TS047_RoL_RNA_442
        87.8%
        25.5M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_442_1
        73.0%
        46.0%
        101bp
        101bp
        18%
        29.1M
        1.1%
        73.0%
        46.0%
        100bp
        100bp
        18%
        29.0M
        TS047_RoL_RNA_442_2
        72.8%
        46.0%
        101bp
        101bp
        18%
        29.1M
        1.2%
        72.9%
        46.0%
        100bp
        100bp
        18%
        29.0M
        TS047_RoL_RNA_46
        95.2%
        24.5M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_468
        85.8%
        23.4M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_468_1
        71.5%
        45.0%
        101bp
        101bp
        9%
        27.3M
        1.2%
        71.5%
        45.0%
        100bp
        100bp
        18%
        27.3M
        TS047_RoL_RNA_468_2
        71.5%
        45.0%
        101bp
        101bp
        18%
        27.3M
        1.3%
        71.5%
        45.0%
        100bp
        100bp
        18%
        27.3M
        TS047_RoL_RNA_469
        89.3%
        27.5M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_469_1
        76.7%
        46.0%
        101bp
        101bp
        9%
        30.8M
        1.1%
        76.7%
        47.0%
        100bp
        100bp
        18%
        30.8M
        TS047_RoL_RNA_469_2
        76.6%
        47.0%
        101bp
        101bp
        18%
        30.8M
        1.3%
        76.7%
        47.0%
        100bp
        100bp
        18%
        30.8M
        TS047_RoL_RNA_46_1
        87.7%
        47.0%
        101bp
        101bp
        9%
        25.7M
        1.3%
        87.7%
        47.0%
        99bp
        100bp
        18%
        25.7M
        TS047_RoL_RNA_46_2
        87.6%
        47.0%
        101bp
        101bp
        18%
        25.7M
        1.4%
        87.6%
        47.0%
        99bp
        100bp
        18%
        25.7M
        TS047_RoL_RNA_477
        86.4%
        24.5M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_477_1
        68.1%
        46.0%
        101bp
        101bp
        18%
        28.4M
        1.1%
        68.1%
        46.0%
        100bp
        100bp
        18%
        28.4M
        TS047_RoL_RNA_477_2
        68.2%
        46.0%
        101bp
        101bp
        18%
        28.4M
        1.2%
        68.2%
        46.0%
        100bp
        100bp
        18%
        28.4M
        TS047_RoL_RNA_478
        86.6%
        24.9M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_478_1
        72.5%
        46.0%
        101bp
        101bp
        9%
        28.8M
        1.1%
        72.5%
        46.0%
        100bp
        100bp
        18%
        28.8M
        TS047_RoL_RNA_478_2
        72.4%
        46.0%
        101bp
        101bp
        18%
        28.8M
        1.2%
        72.4%
        46.0%
        100bp
        100bp
        18%
        28.8M
        TS047_RoL_RNA_498
        85.9%
        24.0M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_498_1
        70.1%
        46.0%
        101bp
        101bp
        9%
        28.0M
        1.2%
        70.1%
        46.0%
        100bp
        100bp
        18%
        28.0M
        TS047_RoL_RNA_498_2
        70.2%
        46.0%
        101bp
        101bp
        18%
        28.0M
        1.3%
        70.3%
        46.0%
        100bp
        100bp
        18%
        28.0M
        TS047_RoL_RNA_500
        88.3%
        24.8M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_500_1
        73.1%
        46.0%
        101bp
        101bp
        9%
        28.1M
        1.1%
        73.2%
        46.0%
        100bp
        100bp
        27%
        28.1M
        TS047_RoL_RNA_500_2
        72.9%
        46.0%
        101bp
        101bp
        27%
        28.1M
        1.2%
        72.9%
        46.0%
        100bp
        100bp
        27%
        28.1M
        TS047_RoL_RNA_502
        84.0%
        21.3M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_502_1
        68.8%
        45.0%
        101bp
        101bp
        9%
        25.4M
        0.7%
        68.8%
        45.0%
        100bp
        100bp
        18%
        25.3M
        TS047_RoL_RNA_502_2
        68.9%
        45.0%
        101bp
        101bp
        27%
        25.4M
        0.9%
        69.0%
        45.0%
        100bp
        100bp
        27%
        25.3M
        TS047_RoL_RNA_506
        87.8%
        25.2M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_506_1
        73.8%
        46.0%
        101bp
        101bp
        9%
        28.7M
        1.1%
        73.8%
        46.0%
        100bp
        100bp
        18%
        28.7M
        TS047_RoL_RNA_506_2
        73.5%
        46.0%
        101bp
        101bp
        18%
        28.7M
        1.3%
        73.6%
        46.0%
        100bp
        100bp
        18%
        28.7M
        TS047_RoL_RNA_51
        86.6%
        21.2M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_51_1
        71.1%
        46.0%
        101bp
        101bp
        18%
        24.5M
        1.2%
        71.1%
        46.0%
        100bp
        100bp
        27%
        24.5M
        TS047_RoL_RNA_51_2
        71.2%
        46.0%
        101bp
        101bp
        18%
        24.5M
        1.3%
        71.3%
        46.0%
        100bp
        100bp
        18%
        24.5M
        TS047_RoL_RNA_526
        92.1%
        34.2M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_526_1
        78.7%
        47.0%
        101bp
        101bp
        9%
        37.2M
        1.0%
        78.7%
        47.0%
        100bp
        100bp
        18%
        37.2M
        TS047_RoL_RNA_526_2
        78.6%
        47.0%
        101bp
        101bp
        18%
        37.2M
        1.2%
        78.7%
        47.0%
        100bp
        100bp
        18%
        37.2M
        TS047_RoL_RNA_528
        86.0%
        29.5M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_528_1
        74.1%
        46.0%
        101bp
        101bp
        18%
        34.3M
        1.1%
        74.1%
        46.0%
        100bp
        100bp
        18%
        34.3M
        TS047_RoL_RNA_528_2
        74.0%
        46.0%
        101bp
        101bp
        18%
        34.3M
        1.3%
        74.0%
        46.0%
        100bp
        100bp
        18%
        34.3M
        TS047_RoL_RNA_530
        85.7%
        22.0M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_530_1
        71.9%
        45.0%
        101bp
        101bp
        18%
        25.7M
        1.2%
        71.9%
        45.0%
        100bp
        100bp
        18%
        25.7M
        TS047_RoL_RNA_530_2
        71.9%
        45.0%
        101bp
        101bp
        18%
        25.7M
        1.3%
        71.9%
        46.0%
        100bp
        100bp
        18%
        25.7M
        TS047_RoL_RNA_532
        88.6%
        23.3M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_532_1
        72.5%
        46.0%
        101bp
        101bp
        9%
        26.3M
        1.1%
        72.5%
        46.0%
        100bp
        100bp
        18%
        26.3M
        TS047_RoL_RNA_532_2
        72.5%
        46.0%
        101bp
        101bp
        18%
        26.3M
        1.2%
        72.5%
        46.0%
        100bp
        100bp
        18%
        26.3M
        TS047_RoL_RNA_559
        91.8%
        23.5M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_559_1
        78.6%
        47.0%
        101bp
        101bp
        9%
        25.6M
        1.1%
        78.6%
        47.0%
        100bp
        100bp
        18%
        25.6M
        TS047_RoL_RNA_559_2
        78.9%
        47.0%
        101bp
        101bp
        18%
        25.6M
        1.2%
        79.0%
        47.0%
        100bp
        100bp
        18%
        25.6M
        TS047_RoL_RNA_561
        87.7%
        27.0M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_561_1
        75.7%
        46.0%
        101bp
        101bp
        9%
        30.7M
        1.1%
        75.7%
        46.0%
        100bp
        100bp
        18%
        30.7M
        TS047_RoL_RNA_561_2
        75.3%
        46.0%
        101bp
        101bp
        18%
        30.7M
        1.2%
        75.4%
        46.0%
        100bp
        100bp
        18%
        30.7M
        TS047_RoL_RNA_562
        89.3%
        23.5M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_562_1
        76.3%
        46.0%
        101bp
        101bp
        9%
        26.4M
        1.2%
        76.3%
        46.0%
        100bp
        100bp
        18%
        26.4M
        TS047_RoL_RNA_562_2
        76.4%
        46.0%
        101bp
        101bp
        9%
        26.4M
        1.4%
        76.5%
        46.0%
        99bp
        100bp
        9%
        26.4M
        TS047_RoL_RNA_586
        90.5%
        20.4M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_586_1
        80.4%
        46.0%
        101bp
        101bp
        18%
        22.6M
        1.4%
        80.4%
        46.0%
        99bp
        100bp
        27%
        22.6M
        TS047_RoL_RNA_586_2
        80.5%
        46.0%
        101bp
        101bp
        27%
        22.6M
        1.5%
        80.6%
        46.0%
        99bp
        100bp
        27%
        22.6M
        TS047_RoL_RNA_616
        91.4%
        19.6M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_616_1
        79.7%
        46.0%
        101bp
        101bp
        9%
        21.4M
        0.7%
        79.7%
        47.0%
        100bp
        100bp
        27%
        21.4M
        TS047_RoL_RNA_616_2
        80.0%
        46.0%
        101bp
        101bp
        27%
        21.4M
        0.8%
        80.0%
        47.0%
        100bp
        100bp
        27%
        21.4M
        TS047_RoL_RNA_618
        92.1%
        26.1M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_618_1
        80.1%
        47.0%
        101bp
        101bp
        9%
        28.3M
        0.7%
        80.1%
        47.0%
        100bp
        100bp
        18%
        28.3M
        TS047_RoL_RNA_618_2
        80.0%
        47.0%
        101bp
        101bp
        18%
        28.3M
        0.8%
        80.0%
        47.0%
        100bp
        100bp
        18%
        28.3M
        TS047_RoL_RNA_646
        88.3%
        20.1M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_646_1
        72.1%
        46.0%
        101bp
        101bp
        9%
        22.8M
        0.7%
        72.1%
        46.0%
        100bp
        100bp
        18%
        22.8M
        TS047_RoL_RNA_646_2
        72.1%
        46.0%
        101bp
        101bp
        18%
        22.8M
        0.8%
        72.1%
        46.0%
        100bp
        100bp
        18%
        22.8M
        TS047_RoL_RNA_651
        89.4%
        24.5M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_651_1
        75.3%
        46.0%
        101bp
        101bp
        9%
        27.4M
        0.7%
        75.3%
        46.0%
        100bp
        100bp
        18%
        27.4M
        TS047_RoL_RNA_651_2
        75.3%
        46.0%
        101bp
        101bp
        18%
        27.4M
        0.8%
        75.3%
        46.0%
        100bp
        100bp
        18%
        27.4M
        TS047_RoL_RNA_652
        86.0%
        18.6M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_652_1
        70.2%
        46.0%
        101bp
        101bp
        9%
        21.7M
        0.7%
        70.2%
        46.0%
        100bp
        100bp
        18%
        21.7M
        TS047_RoL_RNA_652_2
        70.3%
        46.0%
        101bp
        101bp
        18%
        21.7M
        0.9%
        70.3%
        46.0%
        100bp
        100bp
        18%
        21.7M
        TS047_RoL_RNA_655
        91.8%
        25.7M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_655_1
        77.6%
        47.0%
        101bp
        101bp
        9%
        28.0M
        0.7%
        77.6%
        47.0%
        100bp
        100bp
        18%
        28.0M
        TS047_RoL_RNA_655_2
        77.2%
        47.0%
        101bp
        101bp
        18%
        28.0M
        0.8%
        77.2%
        47.0%
        100bp
        100bp
        18%
        28.0M
        TS047_RoL_RNA_676
        88.1%
        21.8M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_676_1
        73.7%
        46.0%
        101bp
        101bp
        18%
        24.7M
        0.7%
        73.8%
        47.0%
        100bp
        100bp
        27%
        24.7M
        TS047_RoL_RNA_676_2
        73.5%
        47.0%
        101bp
        101bp
        36%
        24.7M
        0.8%
        73.5%
        47.0%
        100bp
        100bp
        36%
        24.7M
        TS047_RoL_RNA_677
        87.4%
        20.9M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_677_1
        71.9%
        46.0%
        101bp
        101bp
        9%
        24.0M
        0.7%
        71.9%
        46.0%
        100bp
        100bp
        18%
        23.9M
        TS047_RoL_RNA_677_2
        71.4%
        46.0%
        101bp
        101bp
        27%
        24.0M
        0.8%
        71.5%
        46.0%
        100bp
        100bp
        27%
        23.9M
        TS047_RoL_RNA_678
        88.2%
        21.1M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_678_1
        72.7%
        46.0%
        101bp
        101bp
        9%
        24.0M
        0.7%
        72.7%
        46.0%
        100bp
        100bp
        18%
        23.9M
        TS047_RoL_RNA_678_2
        72.6%
        46.0%
        101bp
        101bp
        18%
        24.0M
        0.8%
        72.7%
        46.0%
        100bp
        100bp
        18%
        23.9M
        TS047_RoL_RNA_679
        89.3%
        23.2M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_679_1
        73.9%
        46.0%
        101bp
        101bp
        9%
        26.1M
        0.7%
        73.9%
        46.0%
        100bp
        100bp
        18%
        26.0M
        TS047_RoL_RNA_679_2
        74.0%
        46.0%
        101bp
        101bp
        27%
        26.1M
        0.8%
        74.0%
        46.0%
        100bp
        100bp
        27%
        26.0M
        TS047_RoL_RNA_683
        83.9%
        16.9M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_683_1
        72.6%
        45.0%
        101bp
        101bp
        18%
        20.2M
        0.7%
        72.6%
        45.0%
        100bp
        100bp
        27%
        20.2M
        TS047_RoL_RNA_683_2
        72.4%
        45.0%
        101bp
        101bp
        27%
        20.2M
        0.9%
        72.4%
        45.0%
        100bp
        100bp
        27%
        20.2M
        TS047_RoL_RNA_707
        86.1%
        22.8M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_707_1
        70.6%
        46.0%
        101bp
        101bp
        9%
        26.5M
        0.7%
        70.6%
        46.0%
        100bp
        100bp
        18%
        26.5M
        TS047_RoL_RNA_707_2
        70.7%
        46.0%
        101bp
        101bp
        18%
        26.5M
        0.8%
        70.8%
        46.0%
        100bp
        100bp
        18%
        26.5M
        TS047_RoL_RNA_708
        88.4%
        29.8M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_708_1
        75.0%
        46.0%
        101bp
        101bp
        9%
        33.7M
        0.7%
        75.1%
        47.0%
        100bp
        100bp
        18%
        33.7M
        TS047_RoL_RNA_708_2
        74.7%
        46.0%
        101bp
        101bp
        18%
        33.7M
        0.9%
        74.8%
        47.0%
        100bp
        100bp
        18%
        33.7M
        TS047_RoL_RNA_710
        87.8%
        23.3M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_710_1
        74.6%
        46.0%
        101bp
        101bp
        9%
        26.5M
        0.7%
        74.6%
        46.0%
        100bp
        100bp
        18%
        26.5M
        TS047_RoL_RNA_710_2
        74.1%
        46.0%
        101bp
        101bp
        18%
        26.5M
        0.8%
        74.2%
        46.0%
        100bp
        100bp
        18%
        26.5M
        TS047_RoL_RNA_79
        87.2%
        21.6M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_79_1
        76.3%
        45.0%
        101bp
        101bp
        18%
        24.8M
        1.3%
        76.3%
        45.0%
        99bp
        100bp
        18%
        24.8M
        TS047_RoL_RNA_79_2
        76.4%
        45.0%
        101bp
        101bp
        18%
        24.8M
        1.4%
        76.5%
        45.0%
        99bp
        100bp
        18%
        24.8M
        TS047_RoL_RNA_85
        93.9%
        25.5M
        ISR
        100.0%
        0.0
        TS047_RoL_RNA_85_1
        83.4%
        47.0%
        101bp
        101bp
        9%
        27.2M
        1.2%
        83.4%
        47.0%
        100bp
        100bp
        18%
        27.1M
        TS047_RoL_RNA_85_2
        83.3%
        47.0%
        101bp
        101bp
        18%
        27.2M
        1.3%
        83.4%
        47.0%
        100bp
        100bp
        18%
        27.1M

        FastQC (raw)

        This section of the report shows FastQC results before adapter trimming.URL: http://www.bioinformatics.babraham.ac.uk/projects/fastqc

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Created with MultiQC

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Created with MultiQC

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Created with MultiQC

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Created with MultiQC

        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Created with MultiQC

        Sequence Length Distribution

        All samples have sequences of a single length (101bp)

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (e.g. PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Created with MultiQC

        Overrepresented sequences by sample

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        144 samples had less than 1% of reads made up of overrepresented sequences

        Top overrepresented sequences

        Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.

        Showing 0/4 rows and 3/3 columns.
        Overrepresented sequenceReportsOccurrences% of all reads
        GTTCAATCAGCAGTCATGAGGTCTTTGGTGTTCCTGGTGCTCCTTGGAGC
        4
        151690
        0.0040%
        GTCTGATTGAAACTGCAACTTATAACTACATCATGAAACCAGCTGACAAT
        1
        29595
        0.0008%
        CTGATGTTCAGTTCCAAGCTGAAGCTAGACCAAGTGTTGCTCTCCAGACA
        1
        26214
        0.0007%
        GTCGTTTTCAGCAATGGAGGAAACTATCAGTTGCACTCTTGCAGTTGGTT
        1
        26903
        0.0007%

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Created with MultiQC

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        Created with MultiQC

        Cutadapt

        Finds and removes adapter sequences, primers, poly-A tails, and other types of unwanted sequences.URL: https://cutadapt.readthedocs.ioDOI: 10.14806/ej.17.1.200

        Filtered Reads

        This plot shows the number of reads (SE) / pairs (PE) removed by Cutadapt.

        Created with MultiQC

        Trimmed Sequence Lengths (3')

        This plot shows the number of reads with certain lengths of adapter trimmed for the 3' end.

        Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak may be related to adapter length.

        See the cutadapt documentation for more information on how these numbers are generated.

        Created with MultiQC

        FastQC (trimmed)

        This section of the report shows FastQC results after adapter trimming.URL: http://www.bioinformatics.babraham.ac.uk/projects/fastqc

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Created with MultiQC

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Created with MultiQC

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Created with MultiQC

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Created with MultiQC

        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Created with MultiQC

        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Created with MultiQC

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (e.g. PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Created with MultiQC

        Overrepresented sequences by sample

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        144 samples had less than 1% of reads made up of overrepresented sequences

        Top overrepresented sequences

        Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.

        Showing 0/4 rows and 3/3 columns.
        Overrepresented sequenceReportsOccurrences% of all reads
        GTTCAATCAGCAGTCATGAGGTCTTTGGTGTTCCTGGTGCTCCTTGGAGC
        4
        151687
        0.0040%
        GTCGTTTTCAGCAATGGAGGAAACTATCAGTTGCACTCTTGCAGTTGGTT
        1
        26893
        0.0007%
        GTCTGATTGAAACTGCAACTTATAACTACATCATGAAACCAGCTGACAAT
        1
        29595
        0.0008%
        CTGATGTTCAGTTCCAAGCTGAAGCTAGACCAAGTGTTGCTCTCCAGACA
        1
        26214
        0.0007%

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Created with MultiQC

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        Created with MultiQC

        Salmon

        Quantifies expression of transcripts using RNA-seq data.URL: https://combine-lab.github.io/salmonDOI: 10.1038/nmeth.4197

        Created with MultiQC

        Sample relationships

        Plots interrogating sample relationships, based on final count matrices.

        SALMON DESeq2 PCA plot

        Created with MultiQC

        SALMON DESeq2 sample similarity

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        GroupSoftwareVersion
        CUSTOM_GETCHROMSIZESgetchromsizes1.21
        CUSTOM_TX2GENEpython3.10.4
        DESEQ2_QC_PSEUDObioconductor-deseq21.28.0
        r-base4.0.3
        FASTQCfastqc0.12.1
        FQ_LINTfq0.12.0 (2024-07-08)
        FQ_SUBSAMPLEfq0.12.0 (2024-07-08)
        GTF2BEDperl5.26.2
        GTF_FILTERpython3.9.5
        GUNZIP_FASTAgunzip1.1
        GUNZIP_GTFgunzip1.1
        MAKE_TRANSCRIPTS_FASTArsem1.3.1
        star2.7.10a
        SALMON_INDEXsalmon1.10.3
        SALMON_QUANTsalmon1.10.3
        SE_GENEbioconductor-summarizedexperiment1.32.0
        TRIMGALOREcutadapt4.9
        trimgalore0.6.10
        TXIMETA_TXIMPORTbioconductor-tximeta1.20.1
        WorkflowNextflow24.10.4
        nf-core/rnaseqv3.18.0

        nf-core/rnaseq Methods Description

        Suggested text and references to use when describing pipeline usage within the methods section of a publication.URL: https://github.com/nf-core/rnaseq

        Methods

        Data was processed using nf-core/rnaseq v3.18.0 (doi: 10.5281/zenodo.1400710) of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

        The pipeline was executed with Nextflow v24.10.4 (Di Tommaso et al., 2017) with the following command:

        nextflow run /local/cqls/software/nextflow/assets/nf-core-rnaseq_3.18.0/3_18_0 -profile singularity -config nextflow.config -resume -params-file nf-params.json

        References

        • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
        • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
        • Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
        • da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
        Notes:
        • The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
        • You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.

        nf-core/rnaseq Workflow Summary

        - this information is collected when the pipeline is started.URL: https://github.com/nf-core/rnaseq

        Input/output options

        email
        sielerjm@oregonstate.edu
        input
        /nfs3/Sharpton_Lab/prod/prod_restructure/projects/sielerjm/ZF__MajorExp/Transcriptomics/Data/Raw/Samplesheets/samplesheet.csv
        multiqc_title
        ROL_MajExp__rnaseq_051525
        outdir
        /nfs3/Sharpton_Lab/prod/prod_restructure/projects/sielerjm/ZF__MajorExp/Transcriptomics/Results/rnaseq/051525

        Reference genome options

        fasta
        /nfs3/Sharpton_Lab/prod/prod_restructure/projects/sielerjm/ZF__MajorExp/Databases/NCBI/Zebrafish/GCF_049306965.1_GRCz12tu_genomic.fna.gz
        gtf
        /nfs3/Sharpton_Lab/prod/prod_restructure/projects/sielerjm/ZF__MajorExp/Databases/NCBI/Zebrafish/GCF_049306965.1_GRCz12tu_genomic.gtf.gz

        Read filtering options

        bbsplit_fasta_list
        /nfs3/Sharpton_Lab/prod/prod_restructure/projects/sielerjm/ZF__MajorExp/Transcriptomics/Code/Nextflow/bbsplit_refs.csv

        Alignment options

        aligner
        N/A
        pseudo_aligner
        salmon

        Optional outputs

        save_reference
        true

        Process skipping options

        skip_alignment
        true
        skip_umi_extract
        true

        Core Nextflow options

        configFiles
        N/A
        containerEngine
        singularity
        launchDir
        /nfs3/Sharpton_Lab/prod/prod_restructure/projects/sielerjm/ZF__MajorExp/Transcriptomics/Code/Nextflow
        profile
        singularity
        projectDir
        /local/cqls/software/nextflow/assets/nf-core-rnaseq_3.18.0/3_18_0
        runName
        condescending_nightingale
        userName
        sielerjm
        workDir
        /nfs3/Sharpton_Lab/prod/prod_restructure/projects/sielerjm/ZF__MajorExp/Transcriptomics/Code/Nextflow/work